On 4 February 2003, the North Atlantic Council (NAC) decided to extend Operation Active Endeavour to include escorting non-military ships traveling through the Strait of Gibraltar to maintain security in the area and to secure the safe transit of designated Allied ships.

On 29 April 2003, Task Force Endeavour began boarding operations following a NAC decision to enhance the effectiveness of the current naval operation against suspected terrorist activities in the Mediterranean. The boarding operations are conducted in accordance with the rules of international law and are of a compliant nature. Over one hundred and sixty vessels have been boarded (as of 1 June 2010).

Several submarines of the Royal Norwegian Navy Ula class have been deployed in the Mediterranean Sea in support of the NATO Operation Active Endeavour, where their intelligence gathering ability have surpassed expectations. Their operational availability proved to be the highest of all the ships taking part in the operation.

Since its inception, the ships of Active Endeavour have monitored over 100,000 vessels (as of June 2010) and conducted voluntary boardings of over 100. They have also escorted over 480 vessels through the Strait of Gibraltar until escorting was suspended in 2004.

On 4 December 2001, STANAVFORMED ships Aliseo, Formion, and Elrod were called to assist in the rescue of 84 civilians from a stricken oil rig. In high winds and heavy seas, the Italian helicopter of the Aliseo removed all 84 workers from the oil rig in 14 flights.

On 2 January 2002, SNFL's Spanish frigate SPS Extremadura and Netherlands oiler HNMLS Amsterdam, the UK naval vessel HMS Beagle and the Greek Coast Guard provided life-saving support to the passengers of a sinking ship in the Eastern Mediterranean off Crete. The Beagle's crew repaired the leaking hull and damaged propulsion to the AYDIN KAPTAN before the weather deteriorated and Greek helicopters began winching the children and women amongst the 254 refugees onboard and carried them to Crete and the Amsterdam. On 3 January 2002, the AYDIN KAPTAN was towed by a Greek fishing vessel, under SNFL escort, to Greek territorial waters.

Vice Admiral Roberto Cesaretti went on to state "Although this event relates to criminals, there is also a message for the terrorists here – we are looking for you, and when we find you – there will be no place to hide."

In an interview with Rear Admiral Richard Leaman OBE, Chief of Staff of the Allied Maritime Component Command - Naples in June 2006, Jane's Navy International was told that the number of frigates involved in the operation had been systematically pared back, with now only three permanent frigates patrolling the Mediterranean, two standby corvettes from Greece and Turkey, and a small submarine force.[3] However, during surge operations the number apparently can rise to 16 ships with forces from Standing NATO Maritime Groups 1 and 2.

Other Mediterranean Dialogue countries expressed interest in collaborating in OAE. An EOL with Morocco was completed on 2 June 2008. It was followed, on 22 October 2009, by a Tactical Memorandum of Understanding defining the modalities of Morocco’s participation in the operation.

An EOL with Georgia was completed on 26 March 2008. The related TMOU was signed on 28 April 2010.

Building on the experience achieved over the years, the operation is now network-based and no longer relies on permanently assigned units. However, it continues to conduct "surge" operations and remains prepared to carry out at-sea inspections. New technologies, exploitation of developments in surveillance and information sharing capabilities, closer cooperation and information sharing with Mediterranean Dialogue (MD) and Partnership for Peace (PfP) countries have enabled a start to the transition from platform-based to network-based operation. A combination of surge operations and standby units will replace permanently deployed forces. Information exchange between NATO and non-NATO contributing nations, law enforcement agencies, international organisations and non-governmental organisations will be enhanced.

HMCS Vancouver deployed on Op Sirius, the Canadian contribution, in November 2011 as it is follow on mission to Operation Unified Protector.